Polygenic Score (PGS) ID: PGS000157

Predicted Trait
Reported Trait Melanoma
Mapped Trait(s) melanoma (EFO_0000756)
Released in PGS Catalog: April 29, 2020
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cGRS_Melanoma
Development Method
Name Pruning and Thresholding (P+T)
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
Variants
Original Genome Build NR
Number of Variants 17
Effect Weight Type Odds Ratio over expected risk
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
318,595 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000438
Europe PMC: 19578365
 1,524 individuals European NR
GWAS Catalog: GCST001124
Europe PMC: 21700618
 8,058 individuals European NR
GWAS Catalog: GCST000198
Europe PMC: 18488026
 1,728 individuals European Q-MEGA
GWAS Catalog: GCST000437
Europe PMC: 19578364
 5,456 individuals European NR
GWAS Catalog: GCST001267
Europe PMC: 21983787
 10,422 individuals European NR
GWAS Catalog: GCST004142
Europe PMC: 28212542
 291,407 individuals European 23andMe

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000488 PSS000277|
European Ancestry|
13,877 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Melanoma — — Odds Ratio (OR; high vs. average risk groups): 1.72 [1.37, 2.16] — —
PPM000477 PSS000277|
European Ancestry|
13,877 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Melanoma — — Mean realative risk: 1.2 [1.14, 1.26]
Wilcoxon test (case vs. control) p-value: 5.99e-11		 — —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000277 Primary tumor samples from TCGA —
[
  • 450 cases
  • , 0 controls
]
 Mean = 59.0 years
Sd = 16.0 years		 European — TCGA —
PSS000277 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —